Ni700 IR/RX port not working with R1

I have a system with an Ni700. I have defined the IR/RX port(5001:5:15) in programming and loaded code with just the device definitions and am having no luck getting the IR in to work. I am not even seeing the IRRX LED light when commands are sent. I have tried both aftermarket IR receivers such as Xantech and the AMX IRX-pp38 http://www.amx.com/products/IRX-PP38.asp with no success.
I have tried changing the IR out on the R1 from 38khz to 255khz, I have tried three different remotes including two R1s and one R2. I have changed the power supply, and tried a second Ni700 master controller. Nothing seems to go. There is no interference from lights etc. I have even tested in the dark to make sure.

Is there some trick to getting this thing to work? Do I need to configure the IR RX port via an online event? I didn't see anything about that in the manual.